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Feng Z, Wang M, Liu Y, Li C, Zhang S, Duan J, Chen J, Qi L, Liu Y, Li H, Wu J, Liu Y, Terzaghi W, Tian F, Zhong B, Fang X, Qian W, Guo Y, Deng XW, Li J. Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor. NATURE PLANTS 2024; 10:798-814. [PMID: 38714768 DOI: 10.1038/s41477-024-01679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/28/2024] [Indexed: 05/10/2024]
Abstract
Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.
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Affiliation(s)
- Ziyi Feng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Meijiao Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Yan Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Cong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jiaqi Chen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanru Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Wu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Feng Tian
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China.
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2
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Viczián A, Nagy F. Phytochrome B phosphorylation expanded: site-specific kinases are identified. THE NEW PHYTOLOGIST 2024; 241:65-72. [PMID: 37814506 DOI: 10.1111/nph.19314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
The phytochrome B (phyB) photoreceptor is a key participant in red and far-red light sensing, playing a dominant role in many developmental and growth responses throughout the whole life of plants. Accordingly, phyB governs diverse signaling pathways, and although our knowledge about these pathways is constantly expanding, our view about their fine-tuning is still rudimentary. Phosphorylation of phyB is one of the relevant regulatory mechanisms, and - despite the expansion of the available methodology - it is still not easy to examine. Phosphorylated phytochromes have been detected using various techniques for decades, but the first phosphorylated phyB residues were only identified in 2013. Since then, concentrated attention has been turned toward the functional role of post-translational modifications in phyB signaling. Very recently in 2023, the first kinases that phosphorylate phyB were identified. These discoveries opened up new research avenues, especially by connecting diverse environmental impacts to light signaling and helping to explain some long-term unsolved problems such as the co-action of Ca2+ and phyB signaling. This review summarizes our recent views about the roles of the identified phosphorylated phyB residues, what we know about the enzymes that modulate the phospho-state of phyB, and how these recent discoveries impact future investigations.
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Affiliation(s)
- András Viczián
- Laboratory of Photo- and Chronobiology, Institute of Plant Biology, Biological Research Centre, Hungarian Research Network (HUN-REN), Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Laboratory of Photo- and Chronobiology, Institute of Plant Biology, Biological Research Centre, Hungarian Research Network (HUN-REN), Szeged, H-6726, Hungary
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3
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Dolde U, Muzzopappa F, Delesalle C, Neveu J, Erdel F, Vert G. LEAFY homeostasis is regulated via ubiquitin-dependent degradation and sequestration in cytoplasmic condensates. iScience 2023; 26:106880. [PMID: 37260753 PMCID: PMC10227421 DOI: 10.1016/j.isci.2023.106880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/06/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
The transcription factor LEAFY (LFY) plays crucial roles in flower development by activating floral homeotic genes. Activation of LFY targets requires the combined action of LFY and the E3 ubiquitin ligase UFO, although the precise underlying mechanism remains unclear. Here, we show that LFY accumulates in biomolecular condensates within the cytoplasm, while recombinant LFY forms condensates with similar properties in vitro. UFO interacts with LFY within these condensates and marks it for degradation. LFY levels in the nucleus are buffered against changes in total LFY levels induced by proteasome inhibition, UFO overexpression, or mutation of lysine residues in a disordered region of LFY. Perturbation of cytoplasmic LFY condensates by 1,6-hexanediol treatment induces the relocalization of LFY to the nucleus and the subsequent activation of the LFY target AP3 in flowers. Our data suggest that nucleocytoplasmic partitioning, condensation, and ubiquitin-dependent degradation regulate LFY levels in the nucleus to control its activity.
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Affiliation(s)
- Ulla Dolde
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Fernando Muzzopappa
- Center for Integrative Biology (CBI), Molecular, Cellular and Developmental Biology UMR5077 CNRS/University of Toulouse, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex, France
| | - Charlotte Delesalle
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Julie Neveu
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | - Fabian Erdel
- Center for Integrative Biology (CBI), Molecular, Cellular and Developmental Biology UMR5077 CNRS/University of Toulouse, 169 Avenue Marianne Grunberg-Manago, 31062 Toulouse Cedex, France
| | - Grégory Vert
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University of Toulouse/Toulouse-INP, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
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4
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Cai X, Huq E. Exciting new discoveries in phytochrome-mediated light signaling pathways. Sci Bull (Beijing) 2023:S2095-9273(23)00315-8. [PMID: 37211490 DOI: 10.1016/j.scib.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- Xingbo Cai
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin 78712, USA.
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5
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Liu X, Jiang W, Li Y, Nie H, Cui L, Li R, Tan L, Peng L, Li C, Luo J, Li M, Wang H, Yang J, Zhou B, Wang P, Liu H, Zhu JK, Zhao C. FERONIA coordinates plant growth and salt tolerance via the phosphorylation of phyB. NATURE PLANTS 2023; 9:645-660. [PMID: 37012430 DOI: 10.1038/s41477-023-01390-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Phosphorylation modification is required for the modulation of phytochrome B (phyB) thermal reversion, but the kinase(s) that phosphorylate(s) phyB and the biological significance of the phosphorylation are still unknown. Here we report that FERONIA (FER) phosphorylates phyB to regulate plant growth and salt tolerance, and the phosphorylation not only regulates dark-triggered photobody dissociation but also modulates phyB protein abundance in the nucleus. Further analysis indicates that phosphorylation of phyB by FER is sufficient to accelerate the conversion of phyB from the active form (Pfr) to the inactive form (Pr). Under salt stress, FER kinase activity is inhibited, leading to delayed photobody dissociation and increased phyB protein abundance in the nucleus. Our data also show that phyB mutation or overexpression of PIF5 attenuates growth inhibition and promotes plant survival under salt stress. Together, our study not only reveals a kinase that controls phyB turnover via a signature of phosphorylation, but also provides mechanistic insights into the role of the FER-phyB module in coordinating plant growth and stress tolerance.
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Affiliation(s)
- Xin Liu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wei Jiang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yali Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Haozhen Nie
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Lina Cui
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Rongxia Li
- Shanghai Bioprofile Technology Company Ltd, Shanghai, China
| | - Li Tan
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinyan Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ming Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Bing Zhou
- University of the Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, China.
| | - Chunzhao Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
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Zhang H, Hu X, Yang B, Zhou Q. Effective cross-linking strategy for graphene oxide membrane with high structural stability and enhanced separation performance. NANOTECHNOLOGY 2023; 34:235701. [PMID: 36867868 DOI: 10.1088/1361-6528/acc111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
In order to solve the poor structural stability of graphene oxide (GO) membrane, a facile and effective cross-linking technology was employed to create a high-performance GO membrane. Herein, DL-Tyrosine/amidinothiourea and (3-Aminopropyl) triethoxysilane were used to crosslink GO nanosheets and porous alumina substrate, respectively. The group evolution of GO with different cross-linking agents was detected via Fourier transform infrared spectroscopy. Ultrasonic treatment and soaking experiment were conducted to explore the structural stability of the different membranes. The GO membrane cross-linked with amidinothiourea exhibits exceptional structural stability. Meanwhile, the membrane has superior separation performance, with the pure water flux reaching approximately 109.6 l·m-2·h-1·bar-1. During the treatment of 0.1 g l-1NaCl solution, its permeation flux and rejection for NaCl are about 86.8 l·m-2·h-1·bar-1and 50.8%, respectively. The long-term filtration experiment also demonstrates that the membrane exhibits great operational stability. All these indicate the cross-linking graphene oxide membrane has promising potential applications in water treatment.
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Affiliation(s)
- Huaitao Zhang
- Key Laboratory of Inorganic Membrane, Jingdezhen Ceramic University, Jingdezhen 333001, People's Republic of China
| | - Xuebing Hu
- Key Laboratory of Inorganic Membrane, Jingdezhen Ceramic University, Jingdezhen 333001, People's Republic of China
| | - Boshen Yang
- Key Laboratory of Inorganic Membrane, Jingdezhen Ceramic University, Jingdezhen 333001, People's Republic of China
| | - Qintao Zhou
- Key Laboratory of Inorganic Membrane, Jingdezhen Ceramic University, Jingdezhen 333001, People's Republic of China
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7
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Zhao Y, Shi H, Pan Y, Lyu M, Yang Z, Kou X, Deng XW, Zhong S. Sensory circuitry controls cytosolic calcium-mediated phytochrome B phototransduction. Cell 2023; 186:1230-1243.e14. [PMID: 36931246 DOI: 10.1016/j.cell.2023.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/23/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023]
Abstract
Although Ca2+ has long been recognized as an obligatory intermediate in visual transduction, its role in plant phototransduction remains elusive. Here, we report a Ca2+ signaling that controls photoreceptor phyB nuclear translocation in etiolated seedlings during dark-to-light transition. Red light stimulates acute cytosolic Ca2+ increases via phyB, which are sensed by Ca2+-binding protein kinases, CPK6 and CPK12 (CPK6/12). Upon Ca2+ activation, CPK6/12 in turn directly interact with and phosphorylate photo-activated phyB at Ser80/Ser106 to initiate phyB nuclear import. Non-phosphorylatable mutation, phyBS80A/S106A, abolishes nuclear translocation and fails to complement phyB mutant, which is fully restored by combining phyBS80A/S106A with a nuclear localization signal. We further show that CPK6/12 function specifically in the early phyB-mediated cotyledon expansion, while Ser80/Ser106 phosphorylation generally governs phyB nuclear translocation. Our results uncover a biochemical regulatory loop centered in phyB phototransduction and provide a paradigm for linking ubiquitous Ca2+ increases to specific responses in sensory stimulus processing.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
| | - Ying Pan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mohan Lyu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhixuan Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoxia Kou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China.
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8
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Choi DM, Kim SH, Han YJ, Kim JI. Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A. Int J Mol Sci 2023; 24:ijms24032110. [PMID: 36768431 PMCID: PMC9916439 DOI: 10.3390/ijms24032110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Extensive research has been conducted for decades to elucidate the molecular and regulatory mechanisms for phytochrome-mediated light signaling in plants. As a result, tens of downstream signaling components that physically interact with phytochromes are identified, among which negative transcription factors for photomorphogenesis, PHYTOCHROME-INTERACTING FACTORs (PIFs), are well known to be regulated by phytochromes. In addition, phytochromes are also shown to inactivate an important E3 ligase complex consisting of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). This inactivation induces the accumulation of positive transcription factors for plant photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5). Although many downstream components of phytochrome signaling have been studied thus far, it is not fully elucidated which intrinsic activity of phytochromes is necessary for the regulation of these components. It should be noted that phytochromes are autophosphorylating protein kinases. Recently, the protein kinase activity of phytochrome A (phyA) has shown to be important for its function in plant light signaling using Avena sativa phyA mutants with reduced or increased kinase activity. In this review, we highlight the function of phyA as a protein kinase to explain the regulation of plant photoresponses by phyA.
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Affiliation(s)
- Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seong-Hyeon Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
- Correspondence:
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Song P, Yang Z, Guo C, Han R, Wang H, Dong J, Kang D, Guo Y, Yang S, Li J. 14-3-3 proteins regulate photomorphogenesis by facilitating light-induced degradation of PIF3. THE NEW PHYTOLOGIST 2023; 237:140-159. [PMID: 36110045 DOI: 10.1111/nph.18494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
14-3-3s are highly conserved phosphopeptide-binding proteins that play important roles in various developmental and signaling pathways in plants. However, although protein phosphorylation has been proven to be a key mechanism for regulating many pivotal components of the light signaling pathway, the role of 14-3-3 proteins in photomorphogenesis remains largely obscure. PHYTOCHROME-INTERACTING FACTOR3 (PIF3) is an extensively studied transcription factor repressing photomorphogenesis, and it is well-established that upon red (R) light exposure, photo-activated phytochrome B (phyB) interacts with PIF3 and induces its rapid phosphorylation and degradation. PHOTOREGULATORY PROTEIN KINASES (PPKs), a family of nuclear protein kinases, interact with phyB and PIF3 in R light and mediate multisite phosphorylation of PIF3 in vivo. Here, we report that two members of the 14-3-3 protein family, 14-3-3λ and κ, bind to a serine residue in the bHLH domain of PIF3 that can be phosphorylated by PPKs, and act as key positive regulators of R light-induced photomorphogenesis. Moreover, 14-3-3λ and κ preferentially interact with photo-activated phyB and promote the phyB-PIF3-PPK complex formation, thereby facilitating phyB-induced phosphorylation and degradation of PIF3 upon R light exposure. Together, our data demonstrate that 14-3-3λ and κ work in close concert with the phyB-PIF3 module to regulate light signaling in Arabidopsis.
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Affiliation(s)
- Pengyu Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zidan Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Can Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Run Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huaichang Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jie Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Dingming Kang
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Fang W, Vellutini E, Perrella G, Kaiserli E. TANDEM ZINC-FINGER/PLUS3 regulates phytochrome B abundance and signaling to fine-tune hypocotyl growth. THE PLANT CELL 2022; 34:4213-4231. [PMID: 35929801 PMCID: PMC9614508 DOI: 10.1093/plcell/koac236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/28/2022] [Indexed: 05/19/2023]
Abstract
TANDEM ZINC-FINGER/PLUS3 (TZP) is a transcriptional regulator that acts at the crossroads of light and photoperiodic signaling. Here, we unveil a role for TZP in fine-tuning hypocotyl elongation under red light and long-day conditions. We provide genetic evidence for a synergistic action between TZP and PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) in regulating the protein abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and downstream gene expression in response to red light and long days (LDs). Furthermore, we show that TZP is a positive regulator of the red/far-red light receptor and thermosensor phytochrome B (phyB) by promoting phyB protein abundance, nuclear body formation, and signaling. Our data therefore assign a function to TZP in regulating two key red light signaling components, phyB and PIF4, but also uncover a new role for PCH1 in regulating hypocotyl elongation in LDs. Our findings provide a framework for the understanding of the mechanisms associated with the TZP signal integration network and their importance for optimizing plant growth and adaptation to a changing environment.
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Affiliation(s)
- Weiwei Fang
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Elisa Vellutini
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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11
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Lindbäck LN, Hu Y, Ackermann A, Artz O, Pedmale UV. UBP12 and UBP13 deubiquitinases destabilize the CRY2 blue light receptor to regulate Arabidopsis growth. Curr Biol 2022; 32:3221-3231.e6. [PMID: 35700731 PMCID: PMC9378456 DOI: 10.1016/j.cub.2022.05.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/22/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.
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Affiliation(s)
- Louise N Lindbäck
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Yuzhao Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Amanda Ackermann
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Oliver Artz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Ullas V Pedmale
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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12
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Song W, Hu L, Ma Z, Yang L, Li J. Importance of Tyrosine Phosphorylation in Hormone-Regulated Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23126603. [PMID: 35743047 PMCID: PMC9224382 DOI: 10.3390/ijms23126603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 02/01/2023] Open
Abstract
Protein phosphorylation is the most frequent post-translational modification (PTM) that plays important regulatory roles in a wide range of biological processes. Phosphorylation mainly occurs on serine (Ser), threonine (Thr), and tyrosine (Tyr) residues, with the phosphorylated Tyr sites accounting for ~1–2% of all phosphorylated residues. Tyr phosphorylation was initially believed to be less common in plants compared to animals; however, recent investigation indicates otherwise. Although they lack typical protein Tyr kinases, plants possess many dual-specificity protein kinases that were implicated in diverse cellular processes by phosphorylating Ser, Thr, and Tyr residues. Analyses of sequenced plant genomes also identified protein Tyr phosphatases and dual-specificity protein phosphatases. Recent studies have revealed important regulatory roles of Tyr phosphorylation in many different aspects of plant growth and development and plant interactions with the environment. This short review summarizes studies that implicated the Tyr phosphorylation in biosynthesis and signaling of plant hormones.
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Affiliation(s)
- Weimeng Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Li Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Zhihui Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Lei Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (W.S.); (L.H.); (Z.M.); (L.Y.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence:
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13
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Du Y, Xie S, Wang Y, Ma Y, Jia B, Liu X, Rong J, Li R, Zhu X, Song CP, Tao WA, Wang P. Low molecular weight protein phosphatase APH mediates tyrosine dephosphorylation and ABA response in Arabidopsis. STRESS BIOLOGY 2022; 2:23. [PMID: 35935594 PMCID: PMC9345830 DOI: 10.1007/s44154-022-00041-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/17/2022] [Indexed: 02/02/2023]
Abstract
Low molecular weight protein tyrosine phosphatase (LWM-PTP), also known as acid phosphatase, is a highly conserved tyrosine phosphatase in living organisms. However, the function of LWM-PTP homolog has not been reported yet in plants. Here, we revealed a homolog of acid phosphatase, APH, in Arabidopsis plants, is a functional protein tyrosine phosphatase. The aph mutants are hyposensitive to ABA in post-germination growth. We performed an anti-phosphotyrosine antibody-based quantitative phosphoproteomics in wild-type and aph mutant and identified hundreds of putative targets of APH, including multiple splicing factors and other transcriptional regulators. Consistently, RNA-seq analysis revealed that the expression of ABA-highly-responsive genes is suppressed in aph mutants. Thus, APH regulates the ABA-responsive gene expressions by regulating the tyrosine phosphorylation of multiple splicing factors and other post-transcriptional regulators. We also revealed that Tyr383 in RAF9, a member of B2 and B3 RAF kinases that phosphorylate and activate SnRK2s in the ABA signaling pathway, is a direct target site of APH. Phosphorylation of Tyr383 is essential for RAF9 activity. Our results uncovered a crucial function of APH in ABA-induced tyrosine phosphorylation in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1007/s44154-022-00041-6.
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Affiliation(s)
- Yanyan Du
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907 USA
| | - Yubei Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Ma
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bei Jia
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xue Liu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jingkai Rong
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Rongxia Li
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xiaohong Zhu
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - W. Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- State Key Laboratory of Crop Stress Adaption and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004 China
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14
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Viczián A, Klose C, Hiltbrunner A, Nagy F. Editorial: Plant Phytochromes: From Structure to Signaling and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:811379. [PMID: 34956300 PMCID: PMC8698484 DOI: 10.3389/fpls.2021.811379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Affiliation(s)
- András Viczián
- Biological Research Centre, Institute of Plant Biology, Laboratory of Photo- and Chronobiology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, University of Freiburg, Freiburg im Breisgau, Germany
- Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg im Breisgau, Germany
| | - Ferenc Nagy
- Biological Research Centre, Institute of Plant Biology, Laboratory of Photo- and Chronobiology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
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15
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von Horsten S, Essen LO. Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5. FRONTIERS IN PLANT SCIENCE 2021; 12:733069. [PMID: 34721460 PMCID: PMC8551457 DOI: 10.3389/fpls.2021.733069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Phytochrome activity is not only controlled by light but also by post-translational modifications, e. g. phosphorylation. One of the phosphatases responsible for plant phytochrome dephosphorylation and thereby increased activity is the phytochrome-associated protein phosphatase 5 (PAPP5). We show that PAPP5 recognizes phospho-site mimicking mutants of phytochrome B, when being activated by arachidonic acid (AA). Addition of AA to PAPP5 decreases the α-helical content as tracked by CD-spectroscopy. These changes correspond to conformational changes of the regulatory tetratricopeptide repeats (TPR) region as shown by mapping data from hydrogen deuterium exchange mass spectrometry onto a 3.0 Å crystal structure of PAPP5. Surprisingly, parts of the linker between the TPR and PP2A domains and of the so-called C-terminal inhibitory motif exhibit reduced deuterium uptake upon AA-binding. Molecular dynamics analyses of PAPP5 complexed to a phyB phosphopeptide show that this C-terminal motif remains associated with the TPR region in the substrate bound state, suggesting that this motif merely serves for restricting the orientations of the TPR region relative to the catalytic PP2A domain. Given the high similarity to mammalian PP5 these data from a plant ortholog show that the activation mode of these PPP-type protein phosphatases is highly conserved.
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Affiliation(s)
- Silke von Horsten
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University, Marburg, Germany
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16
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Li C, Luo Y, Jin M, Sun S, Wang Z, Li Y. Response of Lignin Metabolism to Light Quality in Wheat Population. FRONTIERS IN PLANT SCIENCE 2021; 12:729647. [PMID: 34589105 PMCID: PMC8473876 DOI: 10.3389/fpls.2021.729647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/13/2021] [Indexed: 06/02/2023]
Abstract
The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.
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Affiliation(s)
| | | | | | | | | | - Yong Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai’an, China
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17
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PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nat Genet 2021; 53:955-961. [PMID: 34140685 PMCID: PMC9169284 DOI: 10.1038/s41588-021-00882-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 05/11/2021] [Indexed: 01/26/2023]
Abstract
The interplay between light receptors and PHYTOCHROME-INTERACTING FACTORs (PIFs) serves as a regulatory hub that perceives and integrates environmental cues into transcriptional networks of plants1,2. Although occupancy of the histone variant H2A.Z and acetylation of histone H3 have emerged as regulators of environmentally responsive gene networks, how these epigenomic features interface with PIF activity is poorly understood3-7. By taking advantage of rapid and reversible light-mediated manipulation of PIF7 subnuclear localization and phosphorylation, we simultaneously assayed the DNA-binding properties of PIF7, as well as its impact on chromatin dynamics genome wide. We found that PIFs act rapidly to reshape the H2A.Z and H3K9ac epigenetic landscape in response to a change in light quality. Furthermore, we discovered that PIFs achieve H2A.Z removal through direct interaction with EIN6 ENHANCER (EEN), the Arabidopsis thaliana homolog of the chromatin remodeling complex subunit INO80 Subunit 6 (Ies6). Thus, we describe a PIF-INO80 regulatory module that is an intermediate step for allowing plants to change their growth trajectory in response to environmental changes.
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18
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Abstract
The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.
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Affiliation(s)
- Mei-Chun Cheng
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Inyup Paik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
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19
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Burgie ES, Gannam ZTK, McLoughlin KE, Sherman CD, Holehouse AS, Stankey RJ, Vierstra RD. Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families. Proc Natl Acad Sci U S A 2021; 118:e2105649118. [PMID: 34039713 PMCID: PMC8179155 DOI: 10.1073/pnas.2105649118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | | | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63110
| | - Robert J Stankey
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130;
- Department of Genetics, University of Wisconsin, Madison, WI 53706
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20
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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21
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Takala H, Edlund P, Ihalainen JA, Westenhoff S. Tips and turns of bacteriophytochrome photoactivation. Photochem Photobiol Sci 2021; 19:1488-1510. [PMID: 33107538 DOI: 10.1039/d0pp00117a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
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Affiliation(s)
- Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland. and Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland.
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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22
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Hernando CE, Murcia MG, Pereyra ME, Sellaro R, Casal JJ. Phytochrome B links the environment to transcription. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4068-4084. [PMID: 33704448 DOI: 10.1093/jxb/erab037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Phytochrome B (phyB) senses the difference between darkness and light, the level of irradiance, the red/far-red ratio, and temperature. Thanks to these sensory capacities, phyB perceives whether plant organs are buried in the soil, exposed to full sunlight, in the presence of nearby vegetation, and/or under risk of heat stress. In some species, phyB perceives seasonal daylength cues. phyB affects the activity of several transcriptional regulators either by direct physical interaction or indirectly by physical interaction with proteins involved in the turnover of transcriptional regulators. Typically, interaction of a protein with phyB has either negative or positive effects on the interaction of the latter with a third party, this being another protein or DNA. Thus, phyB mediates the context-dependent modulation of the transcriptome underlying changes in plant morphology, physiology, and susceptibility to biotic and abiotic stress. phyB operates as a dynamic switch that improves carbon balance, prioritizing light interception and photosynthetic capacity in open places and the projection of the shoot towards light in the soil, under shade and in warm conditions.
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Affiliation(s)
- Carlos Esteban Hernando
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Mauro Germán Murcia
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Matías Ezequiel Pereyra
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Romina Sellaro
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Jorge José Casal
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
- Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
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23
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Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis. Mol Cell Proteomics 2021; 20:100063. [PMID: 33677124 PMCID: PMC8066427 DOI: 10.1016/j.mcpro.2021.100063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/14/2021] [Accepted: 02/05/2021] [Indexed: 11/27/2022] Open
Abstract
Protein phosphorylation is one of the most prevalent posttranslational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-like kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs. MUT9-LIKE KINASE mutant quantitative proteome and phosphoproteome measured. Changes to proteome and phosphoproteome are specific to genotype and environment. Loss of MLKs alters glucosinolate enzyme abundance and metabolism. Loss of MLKs increases plant sensitivity to UV radiation and DNA damage agents.
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Marquès-Bueno MM, Armengot L, Noack LC, Bareille J, Rodriguez L, Platre MP, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller BK, Nimchuk ZL, Beeckman T, Caño-Delgado AI, Friml J, Jaillais Y. Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism. Curr Biol 2020; 31:228-237.e10. [PMID: 33157019 PMCID: PMC7809621 DOI: 10.1016/j.cub.2020.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/04/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface. MAKR2 is co-expressed with PIN2 and regulates the pace of root gravitropism MAKR2 controls PIN2 asymmetric accumulation at the root level during gravitropism MAKR2 binds to and is a negative regulator of the TMK1 receptor kinase Auxin antagonizes the MAKR2 inhibition of TMK1 by delocalizing MAKR2 in the cytosol
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Affiliation(s)
- Maria Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France; Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Joseph Bareille
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Lesia Rodriguez
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Mengying Liu
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Davy Opdenacker
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Steffen Vanneste
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Lab of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, 119, Yeonsu-gu, Incheon 21985, Republic of Korea
| | - Barbara K Möller
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tom Beeckman
- Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France.
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25
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Isaksson L, Gustavsson E, Persson C, Brath U, Vrhovac L, Karlsson G, Orekhov V, Westenhoff S. Signaling Mechanism of Phytochromes in Solution. Structure 2020; 29:151-160.e3. [PMID: 32916102 DOI: 10.1016/j.str.2020.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the so-called helical spine and a knot in the peptide chain, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module from Deinococcus radiodurans. Photoswitching between the resting and the active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The discovered pathway underpins functional studies of plant phytochromes and may explain photosensing by phytochromes under biological conditions.
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Affiliation(s)
- Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Göran Karlsson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden.
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26
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Hahm J, Kim K, Qiu Y, Chen M. Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities. Nat Commun 2020; 11:1660. [PMID: 32245953 PMCID: PMC7125078 DOI: 10.1038/s41467-020-15526-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
Warm temperature is postulated to induce plant thermomorphogenesis through a signaling mechanism similar to shade, as both destabilize the active form of the photoreceptor and thermosensor phytochrome B (phyB). At the cellular level, shade antagonizes phyB signaling by triggering phyB disassembly from photobodies. Here we report temperature-dependent photobody localization of fluorescent protein-tagged phyB (phyB-FP) in the epidermal cells of Arabidopsis hypocotyl and cotyledon. Our results demonstrate that warm temperature elicits different photobody dynamics than those by shade. Increases in temperature from 12 °C to 27 °C incrementally reduce photobody number by stimulating phyB-FP disassembly from selective thermo-unstable photobodies. The thermostability of photobodies relies on phyB's photosensory module. Surprisingly, elevated temperatures inflict opposite effects on phyB's functions in the hypocotyl and cotyledon despite inducing similar photobody dynamics, indicative of tissue/organ-specific temperature signaling circuitry either downstream of photobody dynamics or independent of phyB. Our results thus provide direct cell biology evidence supporting an early temperature signaling mechanism via dynamic assembly/disassembly of individual photobodies possessing distinct thermostabilities.
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Affiliation(s)
- Joseph Hahm
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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27
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Klose C, Nagy F, Schäfer E. Thermal Reversion of Plant Phytochromes. MOLECULAR PLANT 2020; 13:386-397. [PMID: 31812690 DOI: 10.1016/j.molp.2019.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
Phytochromes are red/far-red reversible photoreceptors essential for plant growth and development. Phytochrome signaling is mediated by the physiologically active far-red-absorbing Pfr form that can be inactivated to the red-absorbing Pr ground state by light-dependent photoconversion or by light-independent thermal reversion, also termed dark reversion. Although the term "dark reversion" is justified by historical reasons and frequently used in the literature, "thermal reversion" more appropriately describes the process of light-independent but temperature-regulated Pfr relaxation that not only occurs in darkness but also in light and is used throughout the review. Thermal reversion is a critical parameter for the light sensitivity of phytochrome-mediated responses and has been studied for decades, often resulting in contradictory findings. Thermal reversion is an intrinsic property of the phytochrome molecules but can be modulated by intra- and intermolecular interactions, as well as biochemical modifications, such as phosphorylation. In this review, we outline the research history of phytochrome thermal reversion, highlighting important predictions that have been made before knowing the molecular basis. We further summarize and discuss recent findings about the molecular mechanisms regulating phytochrome thermal reversion and its functional roles in light and temperature sensing in plants.
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Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
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28
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Viczián A, Ádám É, Staudt AM, Lambert D, Klement E, Romero Montepaone S, Hiltbrunner A, Casal J, Schäfer E, Nagy F, Klose C. Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling. THE NEW PHYTOLOGIST 2020; 225:1635-1650. [PMID: 31596952 DOI: 10.1111/nph.16243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/24/2019] [Indexed: 05/04/2023]
Abstract
Phytochrome B (phyB) is an excellent light quality and quantity sensor that can detect subtle changes in the light environment. The relative amounts of the biologically active photoreceptor (phyB Pfr) are determined by the light conditions and light independent thermal relaxation of Pfr into the inactive phyB Pr, termed thermal reversion. Little is known about the regulation of thermal reversion and how it affects plants' light sensitivity. In this study we identified several serine/threonine residues on the N-terminal extension (NTE) of Arabidopsis thaliana phyB that are differentially phosphorylated in response to light and temperature, and examined transgenic plants expressing nonphosphorylatable and phosphomimic phyB mutants. The NTE of phyB is essential for thermal stability of the Pfr form, and phosphorylation of S86 particularly enhances the thermal reversion rate of the phyB Pfr-Pr heterodimer in vivo. We demonstrate that S86 phosphorylation is especially critical for phyB signaling compared with phosphorylation of the more N-terminal residues. Interestingly, S86 phosphorylation is reduced in light, paralleled by a progressive Pfr stabilization under prolonged irradiation. By investigating other phytochromes (phyD and phyE) we provide evidence that acceleration of thermal reversion by phosphorylation represents a general mechanism for attenuating phytochrome signaling.
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Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
- Research Institute of Translational Biomedicine, Department of Dermatology and Allergology, University of Szeged, H-6726, Szeged, Hungary
| | - Anne-Marie Staudt
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Dorothee Lambert
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Eva Klement
- Laboratory of Proteomics Research, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Sofia Romero Montepaone
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1417DSE, Buenos Aires, Argentina
| | - Andreas Hiltbrunner
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Jorge Casal
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1417DSE, Buenos Aires, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
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29
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Ahsan N, Wilson RS, Rao RSP, Salvato F, Sabila M, Ullah H, Miernyk JA. Mass Spectrometry-Based Identification of Phospho-Tyr in Plant Proteomics. J Proteome Res 2020; 19:561-571. [PMID: 31967836 DOI: 10.1021/acs.jproteome.9b00550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences are absent from plant genomes/kinomes, often leading to the assumption that plant cells lack O-phospho-l-tyrosine (pY). However, recent improvements in sample preparation, coupled with advances in instrument sensitivity and accessibility, have led to results that unequivocally disproved this assumption. Identification of hundreds of pY-peptides/proteins, followed by validation using genomic, molecular, and biochemical approaches, implies previously unappreciated roles for this "animal PTM" in plants. Herein, we review extant results from studies of pY in plants and propose a strategy for preparation and analysis of pY-peptides that will allow a depth of coverage of the plant pY-proteome comparable to that achieved in mammalian systems.
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Affiliation(s)
- Nagib Ahsan
- Division of Biology and Medicine , Brown University , Providence , Rhode Island 02903 , United States.,Center for Cancer Research Development, Proteomics Core Facility , Rhode Island Hospital , Providence , Rhode Island 02903 , United States
| | - Rashaun S Wilson
- Keck Mass Spectrometry & Proteomics Resource , Yale University , New Haven , Connecticut 06511 , United States
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center , Yenepoya University , Mangalore 575018 , India
| | - Fernanda Salvato
- Department of Plant and Microbial Biology, College of Agriculture and Life Sciences , North Carolina State University , Raleigh , North Carolina 27695 , United States
| | - Mercy Sabila
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Hemayet Ullah
- Department of Biology , Howard University , Washington , D.C. 20059 , United States
| | - Ján A Miernyk
- Division of Biochemistry , University of Missouri , Columbia , Missouri 65211 , United States
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30
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Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat Commun 2019; 10:5219. [PMID: 31745087 PMCID: PMC6864062 DOI: 10.1038/s41467-019-13045-0] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.
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31
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GIGANTEA gates gibberellin signaling through stabilization of the DELLA proteins in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:21893-21899. [PMID: 31597737 PMCID: PMC6815129 DOI: 10.1073/pnas.1913532116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock integrates environmental cues with internal biological processes to generate robust rhythms in almost all aspects of plant physiology. The molecular mechanisms underlying the pervasive regulation of plant physiology and development by the circadian clock are still being unraveled. Our study identifies the clock protein GIGANTEA as a key regulator of the response to gibberellins through the regulation of pivotal factors in the signaling of this hormone. Direct modulation of hub components in signaling networks by the circadian clock provides a means through which the oscillator can effectively transduce timing information to an extensive array of physiological pathways. Circadian clock circuitry intersects with a plethora of signaling pathways to adequately time physiological processes to occur at the most appropriate time of the day and year. However, our mechanistic understanding of how the clockwork is wired to its output is limited. Here we uncover mechanistic connections between the core clock component GIGANTEA (GI) and hormone signaling through the modulation of key components of the transduction pathways. Specifically, we show how GI modulates gibberellin (GA) signaling through the stabilization of the DELLA proteins, which act as negative components in the signaling of this hormone. GI function within the GA pathway is required to precisely time the permissive gating of GA sensitivity, thereby determining the phase of GA-regulated physiological outputs.
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32
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Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, Schmitz RJ, Lewsey MG, Chory J, Ecker JR. Epigenetic silencing of a multifunctional plant stress regulator. eLife 2019; 8:e47835. [PMID: 31418686 PMCID: PMC6739875 DOI: 10.7554/elife.47835] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
The central regulator of the ethylene (ET) signaling pathway, which controls a plethora of developmental programs and responses to environmental cues in plants, is ETHYLENE-INSENSITIVE2 (EIN2). Here we identify a chromatin-dependent regulatory mechanism at EIN2 requiring two genes: ETHYLENE-INSENSITIVE6 (EIN6), which is a H3K27me3 demethylase also known as RELATIVE OF EARLY FLOWERING6 (REF6), and EIN6 ENHANCER (EEN), the Arabidopsis homolog of the yeast INO80 chromatin remodeling complex subunit IES6 (INO EIGHTY SUBUNIT). Strikingly, EIN6 (REF6) and the INO80 complex redundantly control the level and the localization of the repressive histone modification H3K27me3 and the histone variant H2A.Z at the 5' untranslated region (5'UTR) intron of EIN2. Concomitant loss of EIN6 (REF6) and the INO80 complex shifts the chromatin landscape at EIN2 to a repressive state causing a dramatic reduction of EIN2 expression. These results uncover a unique type of chromatin regulation which safeguards the expression of an essential multifunctional plant stress regulator.
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Affiliation(s)
- Mark Zander
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Björn C Willige
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Yupeng He
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Thu A Nguyen
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Amber E Langford
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Ramlah Nehring
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Elizabeth Howell
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Robert McGrath
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaUnited States
| | - Anna Bartlett
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Rosa Castanon
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Huaming Chen
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Zhuzhu Zhang
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Florian Jupe
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Anna Stepanova
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Robert J Schmitz
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Mathew G Lewsey
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Joanne Chory
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Ecker
- Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
- Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, Salk Institute for Biological StudiesLa JollaUnited States
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33
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Hoang QTN, Han YJ, Kim JI. Plant Phytochromes and their Phosphorylation. Int J Mol Sci 2019; 20:ijms20143450. [PMID: 31337079 PMCID: PMC6678601 DOI: 10.3390/ijms20143450] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive research over several decades in plant light signaling mediated by photoreceptors has identified the molecular mechanisms for how phytochromes regulate photomorphogenic development, which includes degradation of phytochrome-interacting factors (PIFs) and inactivation of COP1-SPA complexes with the accumulation of master transcription factors for photomorphogenesis, such as HY5. However, the initial biochemical mechanism for the function of phytochromes has not been fully elucidated. Plant phytochromes have long been known as phosphoproteins, and a few protein phosphatases that directly interact with and dephosphorylate phytochromes have been identified. However, there is no report thus far of a protein kinase that acts on phytochromes. On the other hand, plant phytochromes have been suggested as autophosphorylating serine/threonine protein kinases, proposing that the kinase activity might be important for their functions. Indeed, the autophosphorylation of phytochromes has been reported to play an important role in the regulation of plant light signaling. More recently, evidence that phytochromes function as protein kinases in plant light signaling has been provided using phytochrome mutants displaying reduced kinase activities. In this review, we highlight recent advances in the reversible phosphorylation of phytochromes and their functions as protein kinases in plant light signaling.
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Affiliation(s)
- Quyen T N Hoang
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea
| | - Yun-Jeong Han
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea.
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34
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Platre MP, Bayle V, Armengot L, Bareille J, Marquès-Bueno MDM, Creff A, Maneta-Peyret L, Fiche JB, Nollmann M, Miège C, Moreau P, Martinière A, Jaillais Y. Developmental control of plant Rho GTPase nano-organization by the lipid phosphatidylserine. Science 2019; 364:57-62. [PMID: 30948546 DOI: 10.1126/science.aav9959] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/06/2019] [Indexed: 12/28/2022]
Abstract
Rho guanosine triphosphatases (GTPases) are master regulators of cell signaling, but how they are regulated depending on the cellular context is unclear. We found that the phospholipid phosphatidylserine acts as a developmentally controlled lipid rheostat that tunes Rho GTPase signaling in Arabidopsis Live superresolution single-molecule imaging revealed that the protein Rho of Plants 6 (ROP6) is stabilized by phosphatidylserine into plasma membrane nanodomains, which are required for auxin signaling. Our experiments also revealed that the plasma membrane phosphatidylserine content varies during plant root development and that the level of phosphatidylserine modulates the quantity of ROP6 nanoclusters induced by auxin and hence downstream signaling, including regulation of endocytosis and gravitropism. Our work shows that variations in phosphatidylserine levels are a physiological process that may be leveraged to regulate small GTPase signaling during development.
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Affiliation(s)
- Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Laia Armengot
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Joseph Bareille
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Maria Del Mar Marquès-Bueno
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Audrey Creff
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Lilly Maneta-Peyret
- UMR 5200 Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, INRA Bordeaux Aquitaine, 33140 Villenave d'Ornon, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Univ Montpellier, 34090 Montpellier, France
| | - Christine Miège
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Patrick Moreau
- UMR 5200 Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, INRA Bordeaux Aquitaine, 33140 Villenave d'Ornon, France.,Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, University of Bordeaux, 33000 Bordeaux, France
| | | | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France.
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35
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Nohales MA, Liu W, Duffy T, Nozue K, Sawa M, Pruneda-Paz JL, Maloof JN, Jacobsen SE, Kay SA. Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Dev Cell 2019; 49:840-851.e8. [PMID: 31105011 PMCID: PMC6597437 DOI: 10.1016/j.devcel.2019.04.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/16/2019] [Accepted: 04/17/2019] [Indexed: 01/29/2023]
Abstract
Integration of environmental signals with endogenous biological processes is essential for organisms to thrive in their natural environment. Being entrained by periodic environmental changes, the circadian clock incorporates external information to coordinate physiological processes, phasing them to the optimal time of the day and year. Here, we present a pivotal role for the clock component GIGANTEA (GI) as a genome-wide regulator of transcriptional networks mediating growth and adaptive processes in plants. We provide mechanistic details on how GI integrates endogenous timing with light signaling pathways through the global modulation of PHYTOCHROME-INTERACTING FACTORs (PIFs). Gating of the activity of these transcriptional regulators by GI directly affects a wide array of output rhythms, including photoperiodic growth. Furthermore, we uncover a role for PIFs in mediating light input to the circadian oscillator and show how their regulation by GI is required to set the pace of the clock in response to light-dark cycles.
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Affiliation(s)
- Maria A Nohales
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Wanlu Liu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Zhejiang University, University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
| | - Tomas Duffy
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Mariko Sawa
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, La Jolla, CA 92093, USA
| | - Jose L Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, La Jolla, CA 92093, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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36
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Plant photoreceptors: Multi-functional sensory proteins and their signaling networks. Semin Cell Dev Biol 2019; 92:114-121. [PMID: 30946988 DOI: 10.1016/j.semcdb.2019.03.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/29/2019] [Indexed: 12/31/2022]
Abstract
Light is a crucial environmental cue not only for photosynthetic energy production but also for plant growth and development. Plants employ sophisticated methods to detect and interpret information from incoming light. Five classes of photoreceptors have been discovered in the model plant Arabidopsis thaliana. These photoreceptors act either distinctly and/or redundantly in fine-tuning many aspects of plant life cycle. Unlike mobile animals, sessile plants have developed an enormous plasticity to adapt and survive in changing environment. By monitoring different information arising from ambient light, plants precisely regulate downstream signaling pathways to adapt accordingly. Given that changes in the light environment is typically synchronized with other environmental cues such as temperature, abiotic stresses, and seasonal changes, it is not surprising that light signaling pathways are interconnected with multiple pathways to regulate plant physiology and development. Indeed, recent advances in plant photobiology revealed a large network of co-regulation among different photoreceptor signaling pathways as well as other internal signaling pathways (e.g., hormone signaling). In addition, some photoreceptors are directly involved in perception of non-light stimuli (e.g., temperature). Therefore, understanding highly inter-connected signaling networks is essential to explore the photoreceptor functions in plants. Here, we summarize how plants co-ordinate multiple photoreceptors and their internal signaling pathways to regulate a myriad of downstream responses at molecular and physiological levels.
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37
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Abstract
Posttranslational modification (PTM) of proteins occurs during or after translation and in most cases means covalent binding of a functional group to certain amino acid side chains. Among PTMs, phosphorylation is extensively studied for decades. During phosphorylation, a phosphate group is added to the target residue that is dominantly serine, threonine, and tyrosine in eukaryotes. The phosphate group attachment is catalyzed by kinases, whereas the removal of phosphate (dephosphorylation) is performed by phosphatases. Phosphorylation of phytochrome photoreceptors alters light signaling in multiple ways, thus the examination of this PTM is an expanding aspect of light signaling research. Although this chapter presents methods for detecting phosphorylated phytochrome B molecules, it can be applied on other phytochrome species. The first presented protocol of this chapter shows how the phosphorylation state of phytochrome photoreceptors can be monitored in a modified polyacrylamide gel electrophoresis system. The second protocol describes in detail how phosphorylated amino acids of a target molecule can be identified using mass spectrometry analysis.
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Affiliation(s)
- Eva Klement
- Laboratory of Proteomics Research, Biological Research Centre, Szeged, Hungary
| | - Péter Gyula
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - András Viczián
- Plant Biology Institute, Biological Research Centre, Szeged, Hungary.
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38
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Hinge region of Arabidopsis phyA plays an important role in regulating phyA function. Proc Natl Acad Sci U S A 2018; 115:E11864-E11873. [PMID: 30478060 DOI: 10.1073/pnas.1813162115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phytochrome A (phyA) is the only plant photoreceptor that perceives far-red light and then mediates various responses to this signal. Phosphorylation and dephosphorylation of oat phyA have been extensively studied, and it was shown that phosphorylation of a serine residue in the hinge region of oat phyA could regulate the interaction of phyA with its signal transducers. However, little is known about the role of the hinge region of Arabidopsis phyA. Here, we report that three sites in the hinge region of Arabidopsis phyA (i.e., S590, T593, and S602) are essential in regulating phyA function. Mutating all three of these sites to either alanines or aspartic acids impaired phyA function, changed the interactions of mutant phyA with FHY1 and FHL, and delayed the degradation of mutant phyA upon light exposure. Moreover, the in vivo formation of a phosphorylated phyA form was greatly affected by these mutations, while our data indicated that the abundance of this phosphorylated phyA form correlated well with the extent of phyA function, thus suggesting a pivotal role of the phosphorylated phyA in inducing the far-red light response. Taking these data together, our study reveals the important role of the hinge region of Arabidopsis phyA in regulating phyA phosphorylation and function, thus linking specific residues in the hinge region to the regulatory mechanisms of phyA phosphorylation.
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39
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Ding Z, Wei Q, Kihara D. Computing and Visualizing Gene Function Similarity and Coherence with NaviGO. Methods Mol Biol 2018; 1807:113-130. [PMID: 30030807 DOI: 10.1007/978-1-4939-8561-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Gene ontology (GO) is a controlled vocabulary of gene functions across all species, which is widely used for functional analyses of individual genes and large-scale proteomic studies. NaviGO is a webserver for visualizing and quantifying the relationship and similarity of GO annotations. Here, we walk through functionality of the NaviGO webserver ( http://kiharalab.org/web/navigo/ ) using an example input and explain what can be learned from analysis results. NaviGO has four main functions, accessed from each page of the webserver: "GO Parents," "GO Set", "GO Enrichment", and "Protein Set." For a given list of GO terms, the "GO Parents" tab visualizes the hierarchical relationship of GO terms, and the "GO Set" tab calculates six functional similarity and association scores and presents results in a network and a multidimensional scaling plot. For a set of proteins and their associated GO terms, the "GO Enrichment" tab calculates protein GO functional enrichment, while the "Protein Set" tab calculates functional association between proteins. The NaviGO source code can be also downloaded and used locally or integrated into other software pipelines.
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Affiliation(s)
- Ziyun Ding
- Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Qing Wei
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, IN, USA. .,Department of Computer Science, Purdue University, West Lafayette, IN, USA.
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40
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PCH1 and PCHL promote photomorphogenesis in plants by controlling phytochrome B dark reversion. Nat Commun 2017; 8:2221. [PMID: 29263319 PMCID: PMC5738371 DOI: 10.1038/s41467-017-02311-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/18/2017] [Indexed: 11/08/2022] Open
Abstract
Phytochrome B (phyB) is the primary red light photoreceptor in plants, and regulates both growth and development. The relative levels of phyB in the active state are determined by the light conditions, such as direct sunlight or shade, but are also affected by light-independent dark reversion. Dark reversion is a temperature-dependent thermal relaxation process, by which phyB reverts from the active to the inactive state. Here, we show that the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion, resulting in plants with dramatically enhanced light sensitivity. Moreover, far-red and blue light upregulate the expression of PCH1 and PCHL in a phyB independent manner, thereby increasing the response to red light perceived by phyB. PCH1 and PCHL therefore provide a node for the molecular integration of different light qualities by regulation of phyB dark reversion, allowing plants to adapt growth and development to the ambient environment.
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41
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Bürger M, Willige BC, Chory J. A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors. Nat Commun 2017; 8:2201. [PMID: 29259199 PMCID: PMC5736716 DOI: 10.1038/s41467-017-02347-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 01/09/2023] Open
Abstract
Several Pseudomonas and Xanthomonas species are plant pathogens that infect the model organism Arabidopsis thaliana and important crops such as Brassica. Resistant plants contain the infection by rapid cell death of the infected area through the hypersensitive response (HR). A family of highly related α/β hydrolases is involved in diverse processes in all domains of life. Functional details of their catalytic machinery, however, remained unclear. We report the crystal structures of α/β hydrolases representing two different clades of the family, including the protein SOBER1, which suppresses AvrBsT-incited HR in Arabidopsis. Our results reveal a unique hydrophobic anchor mechanism that defines a previously unknown family of protein deacetylases. Furthermore, this study identifies a lid-loop as general feature for substrate turnover in acyl-protein thioesterases and the described family of deacetylases. Furthermore, we found that SOBER1's biological function is not restricted to Arabidopsis thaliana and not limited to suppress HR induced by AvrBsT.
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Affiliation(s)
- Marco Bürger
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Björn C Willige
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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42
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Qiu Y, Pasoreck EK, Reddy AK, Nagatani A, Ma W, Chory J, Chen M. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017. [PMID: 29199270 DOI: 10.1038/s41467-107-02062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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Affiliation(s)
- Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | - Amit K Reddy
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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43
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Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017; 8:1905. [PMID: 29199270 PMCID: PMC5712524 DOI: 10.1038/s41467-017-02062-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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44
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Viczián A, Klose C, Ádám É, Nagy F. New insights of red light-induced development. PLANT, CELL & ENVIRONMENT 2017; 40:2457-2468. [PMID: 27943362 DOI: 10.1111/pce.12880] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 05/14/2023]
Abstract
The red/far-red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever-changing environment. Our understanding of how absorption of a red/far-red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light-grown plants. We discuss how its light-independent inactivation (termed dark/thermal reversion), post-translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light-controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor.
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Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology2/Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
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45
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Burgie ES, Bussell AN, Lye SH, Wang T, Hu W, McLoughlin KE, Weber EL, Li H, Vierstra RD. Photosensing and Thermosensing by Phytochrome B Require Both Proximal and Distal Allosteric Features within the Dimeric Photoreceptor. Sci Rep 2017; 7:13648. [PMID: 29057954 PMCID: PMC5651913 DOI: 10.1038/s41598-017-14037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Phytochromes (Phys) encompass a diverse collection of bilin-containing photoreceptors that help plants and microorganisms perceive light through photointerconversion between red light (Pr) and far-red light (Pfr)-absorbing states. In addition, Pfr reverts thermally back to Pr via a highly enthalpic process that enables temperature sensation in plants and possibly other organisms. Through domain analysis of the Arabidopsis PhyB isoform assembled recombinantly, coupled with measurements of solution size, photoconversion, and thermal reversion, we identified both proximal and distal features that influence all three metrics. Included are the downstream C-terminal histidine kinase-related domain known to promote dimerization and a conserved patch just upstream of an N-terminal Period/Arnt/Sim (PAS) domain, which upon removal dramatically accelerates thermal reversion. We also discovered that the nature of the bilin strongly influences Pfr stability. Whereas incorporation of the native bilin phytochromobilin into PhyB confers robust Pfr → Pr thermal reversion, that assembled with the cyanobacterial version phycocyanobilin, often used for optogenetics, has a dramatically stabilized Pfr state. Taken together, we conclude that Pfr acquisition and stability are impacted by a collection of opposing allosteric features that inhibit or promote photoconversion and reversion of Pfr back to Pr, thus allowing Phys to dynamically measure light, temperature, and possibly time.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Adam N Bussell
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Shu-Hui Lye
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Tong Wang
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,CUNY Advanced Science Research Center, The City University of New York, New York, New York, 10031, USA
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Erin L Weber
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Huilin Li
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA. .,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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46
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Phosphorylation and negative regulation of CONSTITUTIVELY PHOTOMORPHOGENIC 1 by PINOID in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:6617-6622. [PMID: 28584104 DOI: 10.1073/pnas.1702984114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays crucial roles in various cellular processes via its E3 ubiquitin ligase activity in organisms, ranging from fungi to humans. As a key component in regulating various biological events, COP1 itself is precisely controlled at multiple layers. Here, we report a negative regulator of COP1, PINOID (PID), which positively mediates photomorphogenic development. Specifically, PID genetically and physically interacts with COP1 and directly phosphorylates COP1 at Ser20. As a result, this posttranslational modification serves to repress COP1 activity and promote photomorphogenesis. Our findings signify a key regulatory mechanism for precisely maintaining COP1 activity, thereby ensuring appropriate development in plants.
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47
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Velázquez Escobar F, Buhrke D, Fernandez Lopez M, Shenkutie SM, von Horsten S, Essen LO, Hughes J, Hildebrandt P. Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB. FEBS Lett 2017; 591:1258-1265. [DOI: 10.1002/1873-3468.12642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/25/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022]
Affiliation(s)
| | - David Buhrke
- Institut für Chemie; Technische Universität Berlin; Germany
| | | | | | - Silke von Horsten
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
| | - Lars-Oliver Essen
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
- LOEWE Center for Synthetic Microbiology; Philipps-Universität; Marburg Germany
| | - Jon Hughes
- Plant Physiology; Justus-Liebig University Gießen; Giessen Germany
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48
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Mapping light-driven conformational changes within the photosensory module of plant phytochrome B. Sci Rep 2016; 6:34366. [PMID: 27694986 PMCID: PMC5046071 DOI: 10.1038/srep34366] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/09/2016] [Indexed: 12/04/2022] Open
Abstract
Organisms developed different photoreceptors to be able to adapt to changing environmental light conditions. Phytochromes are red/far-red (r/fr) photochromic photoreceptors that belong to the classical photoreceptors along with cryptochromes and phototropins. They convert absorbed light into a biological signal by switching between two states in a light-dependent manner therefore enabling the light control downstream signalling. Their Pfr conformation is the biological active form in plants, but until now only a structure of the ground state (Pr) was solved. Here, the authors provide information about structural changes occurring during photoconversion within phytochrome B and identify possible interaction sites for its N-terminal extension (NTE) utilising hydrogen/deuterium exchange rate analyses of its amide backbone. Especially, the newly identified light-dependency of two regions in the NTE are of particular interest for understanding the involvement of the phytochrome’s NTE in the regulation of its downstream signalling.
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49
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Fíla J, Radau S, Matros A, Hartmann A, Scholz U, Feciková J, Mock HP, Čapková V, Zahedi RP, Honys D. Phosphoproteomics Profiling of Tobacco Mature Pollen and Pollen Activated in vitro. Mol Cell Proteomics 2016; 15:1338-50. [PMID: 26792808 PMCID: PMC4824859 DOI: 10.1074/mcp.m115.051672] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 11/02/2015] [Indexed: 11/06/2022] Open
Abstract
Tobacco mature pollen has extremely desiccated cytoplasm, and is metabolically quiescent. Upon re-hydration it becomes metabolically active and that results in later emergence of rapidly growing pollen tube. These changes in cytoplasm hydration and metabolic activity are accompanied by protein phosphorylation. In this study, we subjected mature pollen, 5-min-activated pollen, and 30-min-activated pollen to TCA/acetone protein extraction, trypsin digestion and phosphopeptide enrichment by titanium dioxide. The enriched fraction was subjected to nLC-MS/MS. We identified 471 phosphopeptides that carried 432 phosphorylation sites, position of which was exactly matched by mass spectrometry. These 471 phosphopeptides were assigned to 301 phosphoproteins, because some proteins carried more phosphorylation sites. Of the 13 functional groups, the majority of proteins were put into these categories: transcription, protein synthesis, protein destination and storage, and signal transduction. Many proteins were of unknown function, reflecting the fact that male gametophyte contains many specific proteins that have not been fully functionally annotated. The quantitative data highlighted the dynamics of protein phosphorylation during pollen activation; the identified phosphopeptides were divided into seven groups based on the regulatory trends. The major group comprised mature pollen-specific phosphopeptides that were dephosphorylated during pollen activation. Several phosphopeptides representing the same phosphoprotein had different regulation, which pinpointed the complexity of protein phosphorylation and its clear functional context. Collectively, we showed the first phosphoproteomics data on activated pollen where the position of phosphorylation sites was clearly demonstrated and regulatory kinetics was resolved.
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Affiliation(s)
- Jan Fíla
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - Sonja Radau
- §Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straβe 6b, 44227 Dortmund, Germany
| | - Andrea Matros
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Anja Hartmann
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Uwe Scholz
- ‖Department of Breeding Research, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Jana Feciková
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - Hans-Peter Mock
- ¶Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetic and Crop Plant Research, Corrensstraβe 3, 06466 Gatersleben, Germany
| | - Věra Čapková
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic
| | - René Peiman Zahedi
- §Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straβe 6b, 44227 Dortmund, Germany
| | - David Honys
- From the ‡Laboratory of Pollen Biology, Institute of Experimental Botany ASCR, v.v.i., Rozvojova 263, 165 00 Praha 6, Czech Republic;
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Yue J, Qin Q, Meng S, Jing H, Gou X, Li J, Hou S. TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1381-97. [PMID: 26704640 PMCID: PMC4775132 DOI: 10.1104/pp.15.01729] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/23/2015] [Indexed: 05/18/2023]
Abstract
In plants, photoreceptors transfer light signals to phytochrome-interacting factors (PIFs), inducing the rapid phosphorylation and degradation of PIFs to promote photomorphogenesis. However, the phosphatase responsible for PIF dephosphorylation remains unknown. In this study, we identified a type 1 protein phosphatase, TOPP4, that is essential for PIF5 protein stability in Arabidopsis (Arabidopsis thaliana). Compared with the wild type, the dominant-negative mutant, topp4-1, displayed reduced hypocotyl length and larger apical hook and cotyledon opening angle under red light. Overexpression of topp4-1 in the wild type led to defects that were similar to those in the topp4-1 mutant. Red light induced phytochrome B (phyB)-dependent TOPP4 expression in hypocotyls. The topp4-1 mutation weakened the closed cotyledon angle of phyB-9 and phyA-211 phyB-9, while overexpression of TOPP4 significantly repressed the short hypocotyls of phyB-green fluorescent protein seedlings, indicating that TOPP4 and phyB function in an antagonistic way during photomorphogenesis. Protein interaction assays and phosphorylation studies demonstrate that TOPP4 interacts directly with PIF5 and dephosphorylates it. Furthermore, TOPP4 inhibits the red light-induced ubiquitination and degradation of PIF5. These findings demonstrate that dephosphorylation of PIF5 by TOPP4 inhibits its ubiquitin-mediated degradation during photomorphogenesis. These data outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses.
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Affiliation(s)
- Jing Yue
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Qin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Siyuan Meng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Huiting Jing
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Suiwen Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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